<tool id="varscan" name="VarScan Readcount" version="2.0">
  <description>To use varscan readcount tool</description>
  <requirements>
    <requirement type="package" version="2.4.4">varscan</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    varscan readcounts '${input}' --output-file '${output}'
  ]]></command>
  <inputs>
    <param name="input" format="pileup" type="data" label="Pileup dataset"/>
  </inputs>
  <outputs>
    <data name="output" format="vcf"/>
  </outputs>
  <help>
    USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
    OPTIONS:
      --output-file   Output file to contain the readcounts
      --min-coverage  Minimum read depth at a position to make a call (default: 1)
      --min-base-qual Minimum base quality at a position to count a read (default: 20)
  </help>
</tool>